How to highlight areas of a desktop recording in video sequence editor
Making the shape in a 2 paint program like GIMP or drawing program like Illustrator is quickest. But with Blender you can animate and iterate more quickly.
You can use a mask from the UV image editor. 


First press F12 to render the present frame into the Image editor.
then change to Mask Mode and create a new mask (name it)





In the VSE add the mask as a strip in the place that you want it to appear 





Select the new mask strip and add a Gaussian Blur, set blur in properties panel (N key) to 10 or more (depending on render resolution).





With Blur effect selected add a curve modifier and make a sharp peak.





Now add a color correction modifier. Set the Gain value to a nice bright color.





Change the mask strip's Blend type (in the properties panel again) to add.


Now you should see a colourful box outline around your region of interest.



What is cool about this approach is that you can animate the shape, color and thickness of the curve during the edit.